knitr::opts_chunk$set(warning = FALSE, message = FALSE)
knitr::opts_chunk$set(fig.width=14, fig.height=8)
library(phyloseq)
library(ggplot2)
library(ggpubr)
library(dplyr)
library(ggVennDiagram)
set.seed(5678)
setwd('/home/alexey/Analysis/2022_StrawPrimers/2023')
ps <- readRDS("ps.RData")
# ps@sam_data %>% View()
ps@sam_data$Compare <- paste(ps@sam_data$Primer, ps@sam_data$Substrate, sep=".")
ps.sub <- subset_samples(ps, Type == "substrate")
plot_vienn <- function(ps, group){
physeq <- prune_taxa(taxa_sums(ps) > 0, ps)
groups <- levels(sample_data(physeq)[[group]] %>% as.factor())
data <- merge_samples(physeq, group) %>%
psmelt() %>%
group_by(Sample, OTU) %>%
summarise(ASVs_abund = list(paste(OTU, 1:sum(Abundance))), Abund = sum(Abundance), .groups='keep') %>%
filter(Abund > 0)
asvs <- data %>% select(Sample, OTU) %>% group_by(Sample) %>% summarise(ASVs = list(OTU)) %>% as.list()
d1 <- asvs[[2]]
names(d1) <- asvs[[1]]
d1
weighted.asvs <- data %>% select(Sample, ASVs_abund) %>% group_by(Sample) %>% summarise(ASVs = list(unlist(ASVs_abund)))
d2 <- weighted.asvs[[2]]
names(d2) <- weighted.asvs[[1]]
d2
list(ggVennDiagram(d1) + ggtitle("ASVs") + scale_fill_distiller(palette = "OrRd", trans = "reverse"),
ggVennDiagram(d2) + ggtitle("Reads") + scale_fill_distiller(palette = "OrRd", trans = "reverse"))
}
p <- plot_vienn(ps.sub %>% subset_samples(Substrate %in% c("BS", "DP", "BG")), "Substrate")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps.sub %>% subset_samples(Substrate %in% c("Oat", "Flx", "Wht")), "Substrate")
ggarrange(p[[1]], p[[2]])
What share breeds takes from substrate and from soil?
p <- plot_vienn(ps %>% subset_samples((Substrate %in% c("DP", "Wht", "")) & (Primer %in% c("DP_Wht", ""))), "Compare")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps %>% subset_samples((Substrate %in% c("DP", "Flx", "")) & (Primer %in% c("DP_FlxN", ""))), "Compare")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps %>% subset_samples((Substrate %in% c("BS", "Wht", "")) & (Primer %in% c("BS_Wht", ""))), "Compare")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps %>% subset_samples((Substrate %in% c("BS", "Flx", "")) & (Primer %in% c("BS_FlxN", ""))), "Compare")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps %>% subset_samples((Substrate %in% c("BG", "Wht", "")) & (Primer %in% c("BG_Wht", ""))), "Compare")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps %>% subset_samples((Substrate %in% c("DP", "Wht", "")) & (Primer %in% c("DP_Wht", ""))), "Compare")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps %>% subset_samples((Substrate %in% c("DP", "")) & (Primer %in% c("DP_Wht", "DP_FlxN", ""))), "Compare")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps %>% subset_samples((Substrate %in% c("BS", "")) & (Primer %in% c("BS_Wht", "BS_FlxN", ""))), "Compare")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps %>% subset_samples((Substrate %in% c("BG", "")) & (Primer %in% c("BG_Wht", "BG_FlxN", ""))), "Compare")
ggarrange(p[[1]], p[[2]])
ps.use <- subset_samples(ps, Type == "use")
p <- plot_vienn(ps.use %>% subset_samples((Substrate == "Oat_Straw") & (Primer %in% c("no", "DP_Wht", "BS_Wht", "BG_Wht"))), "Primer")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps.use %>% subset_samples((Substrate == "Oat_Straw") & (Primer %in% c("no", "DP_FlxN", "BS_FlxN", "BG_FlxN"))), "Primer")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps.use %>% subset_samples((Substrate == "Wheat_Straw_N") & (Primer %in% c("no", "DP_Wht", "BS_Wht", "BG_Wht"))), "Primer")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps.use %>% subset_samples((Substrate == "Wheat_Straw_N") & (Primer %in% c("no", "DP_FlxN", "BS_FlxN", "BG_FlxN"))), "Primer")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps.use %>% subset_samples((Substrate == "Flax_Shover_N") & (Primer %in% c("no", "DP_Wht", "BS_Wht", "BG_Wht"))), "Primer")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps.use %>% subset_samples((Substrate == "Flax_Shover_N") & (Primer %in% c("no", "DP_FlxN", "BS_FlxN", "BG_FlxN"))), "Primer")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps %>% subset_samples((Primer == "DP_Wht") & (Substrate %in% c("Oat_Straw", "Wheat_Straw_N", "Flax_Shover_N", ""))), "Compare")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps %>% subset_samples((Primer == "DP_FlxN") & (Substrate %in% c("Oat_Straw", "Wheat_Straw_N", "Flax_Shover_N", ""))), "Compare")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps %>% subset_samples((Primer == "BS_Wht") & (Substrate %in% c("Oat_Straw", "Wheat_Straw_N", "Flax_Shover_N", ""))), "Compare")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps %>% subset_samples((Primer == "BS_FlxN") & (Substrate %in% c("Oat_Straw", "Wheat_Straw_N", "Flax_Shover_N", ""))), "Compare")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps %>% subset_samples((Primer == "BG_Wht") & (Substrate %in% c("Oat_Straw", "Wheat_Straw_N", "Flax_Shover_N", ""))), "Compare")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps %>% subset_samples((Primer == "BG_FlxN") & (Substrate %in% c("Oat_Straw", "Wheat_Straw_N", "Flax_Shover_N", ""))), "Compare")
ggarrange(p[[1]], p[[2]])
p <- plot_vienn(ps %>% subset_samples((Primer == "DP_FlxN") & (Substrate %in% c("Oat_Straw", "Wheat_Straw_N", "Flax_Shover_N", ""))), "Compare")
ggarrange(p[[1]], p[[2]])